<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
    "http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<link rel="stylesheet" type="text/css" href="logo.css" >


<title>WebLogo - Create </title>
<meta name="author" content="Gavin E. Crooks" >
<meta name="ID" content="$ID:" >

<style type="text/css">
td {
    border-left : white solid 4pt
}
.error { 
    color: #900;
    border-left: red solid +4pt;
}

.err_msg { 
    color: #900;
}

</style>
</head>

<body style="align:center">





<form method="post" action="create.cgi" enctype="multipart/form-data" >
<table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
<tr><td >
<h1> WebLogo 3 : Create</h1>

</td><td align = "right"> 
    &middot; 
  <a href="./">about</a>&nbsp;&middot;
  <a class="selected" href="create.cgi">create</a>&nbsp;&middot; 
  <a href="examples.html">examples</a>&nbsp;&middot; 
  <a href="manual.html">manual</a>&nbsp;&middot; 
<br>
<span style="font-size:small">$version</span>&nbsp;&nbsp;
</td></tr>

<tr><td >
Sequence data
</td><td > 
<input type="file" name="sequences_file"   > 
</td></tr>

<tr><td >
</td><td> 
<span style="font-size:small ">(or paste sequence data below)</span>
</td></tr>



<tr><td colspan='2' ${sequences_err} >
<textarea name="sequences" rows="12" cols ="100" style="width:100%">${sequences}</textarea>
</td></tr>



<tr><td>
</td><td align="right">
<input  style="font-size:large" type="submit" name="cmd_create" value="&nbsp;Create&nbsp;Logo&nbsp;&nbsp;&nbsp;&nbsp;"  > <br>
<span style="font-size:small"><input type="checkbox" name="download" value="false" >Download</span>

</td></tr>
     

<!-- Reset defaults must come after create_logo so that hitting enter creates a logo-->  
<!--
<tr><td>
<input type="submit" name="cmd_reset" value="Reset defaults" >
</td><td  class="err_msg" rowspan="2">
${error_message} &nbsp;
</td></tr>
<tr><td>&nbsp;</td></tr>
-->
<tr><td colspan='2' style="height:30pt;border-left-width:90pt;" class="err_msg">
${error_message}
</td></tr>

    
     
<tr><td ${format_err} >
Output format </td><td>
<select name="format">
<option ${png_print} value="png_print">PNG</option>
<option ${png} value="png">PNG (low res.)</option>
<option ${jpeg} value="jpeg">JPEG (low res.)</option>
<option ${eps} value="eps">EPS (vector)</option>
<option ${pdf} value="pdf">PDF (vector)</option>
<option ${txt} value="txt">Data (plain text)</option> 
</select> 

</td></tr>

<tr><td ${size_err} >
Logo size 
</td><td >
<select name="size" >
<option ${small} >small</option>
<option ${medium}>medium</option>
<option ${large} >large</option>
</select> 
</td></tr>


<tr><td ${stacks_per_line_err}>
    Stacks per line
</td><td>
<input type="text" name="stacks_per_line" value="${stacks_per_line}" size="4" maxlength="4" >
</td></tr>

<tr><td ${alphabet_err}>
Sequence type </td><td>

<select name="alphabet">
<option ${alphabet_auto} value="alphabet_auto" >auto</option>
<option ${alphabet_protein} value="alphabet_protein">protein</option>
<option ${alphabet_dna} value="alphabet_dna">dna</option>
<option ${alphabet_rna} value="alphabet_rna">rna</option>
</select> 
</td></tr>

<tr><td>
Units </td><td>
<select name="unit_name"  >
<option ${probability} >probability</option>
<option ${bits} >bits</option>
<option ${nats} >nats</option>
<option ${kT} >kT</option>
<option ${kJ_mol} >kJ/mol</option>
<option ${kcal_mol} >kcal/mol</option>
</select> 

</td></tr>

<tr><td ${first_index_err}>
First position number
</td><td>
<input  type="text" name="first_index" value="${first_index}" size="4" maxlength="80" >
</td></tr>

<tr><td ${logo_range_err} >
Logo range </td><td>
<input type="text" name="logo_start" value="${logo_start}" size="4" maxlength="80" > - <input type="text" name="logo_end"  value="${logo_end}" size="4" maxlength="80" >
</td></tr>



<tr><td ${composition_err}>
Composition
</td><td>
<select name="composition" >
<option ${comp_none} value = "comp_none" >No adjustment for composition</option>
<option ${comp_auto} value = "comp_auto" >auto</option>
<option ${comp_equiprobable} value = "comp_equiprobable"  >equiprobable</option>
<option ${comp_CG} value="comp_CG" >Percentage CG &#8658;</option>
<option ${comp_Celegans} value="comp_Celegans" >C. elegans (36%) </option>
<option ${comp_Dmelanogaster} value="comp_Dmelanogaster" >D. melanogaster (43%)</option>
<option ${comp_Ecoli} value="comp_Ecoli" >E. coli (50.5%) </option>
<option ${comp_Hsapiens} value="comp_Hsapiens" >H. sapiens (40%) </option>
<option ${comp_Mmusculus}  value="comp_Mmusculus" >M. musculus (42%)</option>
<option ${comp_Scerevisiae} value="comp_Scerevisiae" >S. cerevisiae (38%) </option>
</select>
or
<input type="text" name="percentCG" value="${percentCG}" size="4" maxlength="8"   >  % CG
</td></tr>


<tr><td>
Error bars
</td><td>
 <input type="checkbox" name="show_errorbars" value="true" ${show_errorbars}  >
</td></tr>
 





<tr    ><td ${logo_title_err}>
Title
</td><td >
<input   type="text"  name="logo_title"  size="52" maxlength="80" value="${logo_title}" > 
</td></tr>

<tr><td>
Figure label</td><td>
<input type="text" name="logo_label"  value="${logo_label}" size="4" maxlength="100" > 
</td></tr>


<tr><td>
X-axis
</td><td>
<input type="checkbox" name="show_xaxis" value="true" ${show_xaxis} >
Label: 
<input type="text" name="xaxis_label"  value="${xaxis_label}" size="20" maxlength="100" >  
</td></tr>


<tr><td>
Y-axis
</td><td>
<input type="checkbox" name="show_yaxis" value="true" ${show_yaxis} > 
Label: <input type="text" name="yaxis_label" value="${yaxis_label}" size="20" maxlength="32" >  

</td></tr>

<tr><td ${yaxis_scale_err} >
Y-axis scale:
</td><td>
<input type="text" name="yaxis_scale"  value="${yaxis_scale}" size="4" maxlength="100"  > 
</td></tr>

 <tr><td ${yaxis_tic_interval_err} >
Y-axis tic spacing:
</td><td>
<input type="text" name="yaxis_tic_interval" value="${yaxis_tic_interval}"  size="4" maxlength="100"  > 
</td></tr>


<tr><td>
Sequence end labels
</td><td>
<input type="checkbox" name="show_ends" value="true" ${show_ends} > 
</td></tr>
  
<tr><td>
Version fineprint 
  </td><td>
<input type="checkbox" name="show_fineprint" value="true" ${show_fineprint} >
</td></tr>




<tr><td  ${color_scheme_err}>Color scheme
</td><td>
<select name="color_scheme"  >
<option ${color_auto} value="color_auto">Auto</option>
<option ${color_monochrome} value="color_monochrome" >Monochrome</option>
<option ${color_base_pairing} value="color_base_pairing">Base pairing (NA default)</option>
<option ${color_classic} value="color_classic">Classic (NA)</option>
<option ${color_hydrophobicity} value="color_hydrophobicity">Hydrophobicity (AA default)</option>
<option ${color_chemistry} value="color_chemistry">Chemistry (AA)</option>
<option ${color_charge} value="color_charge">Charge (AA)</option>
<option ${color_custom} value="color_custom">Custom (Specify below)</option>
</select> 
<!--&nbsp; Color key:
<input type="checkbox" name="show_color_key" value="true" ${show_color_key} disabled >
-->
</td></tr>

<tr><td></td><td>
<table cellpadding="0" cellspacing="0"  style="font-size:small">
<tr>
<td>Symbols</td><td>Color</td> <!--<td>Description</td>-->
</tr>

<tr >
<td ${color0_err}><input name="symbols0" type="text"  size="16" maxlength="64" value="${symbols0}"></td>
<td><input name="color0" type="text"  size="16" maxlength="64"  value="${color0}"></td>
<!--<td><input name="desc0"  size="16" maxlength="64"  value="${desc0}"></td> -->
</tr>

<tr >
<td ${color1_err}><input name="symbols1" type="text"  size="16" maxlength="64" value="${symbols1}"></td>
<td><input name="color1" type="text"  size="16" maxlength="64"  value="${color1}"></td>
<!--<td><input name="desc1"  size="16" maxlength="64"  value="${desc1}"></td>-->
</tr>

<tr>
<td ${color2_err}><input name="symbols2" type="text"  size="16" maxlength="64" value="${symbols2}"></td>
<td><input name="color2" type="text"  size="16" maxlength="64"  value="${color2}"></td>
<!--<td><input name="desc2"  size="16" maxlength="64"  value="${desc2}"></td>-->
</tr>

<tr>
<td ${color3_err}><input name="symbols3" type="text"  size="16" maxlength="64" value="${symbols3}"></td>
<td><input name="color3" type="text"  size="16" maxlength="64"  value="${color3}"></td>
<!--<td><input name="desc3"  size="16" maxlength="64"  value="${desc3}"></td>-->
</tr>

<tr>
<td ${color4_err}><input name="symbols4" type="text"  size="16" maxlength="64" value="${symbols4}"></td>
<td><input name="color4" type="text"  size="16" maxlength="64"  value="${color4}"></td>
<!--<td><input name="desc4"  size="16" maxlength="64"  value="${desc4}"></td>-->
</tr>



</table>
</td></tr>

 <tr><td>
&nbsp; 
</td><td>
&nbsp;
</td></tr>
      
<tr><td>
<input type="submit" name="cmd_reset" value="Reset defaults" >
</td><td align="right">
<input  style="font-size:large" type="submit" name="cmd_create" value="&nbsp;Create&nbsp;Logo&nbsp;&nbsp;&nbsp;&nbsp;"  >
</td></tr>
     
     


</table>
</form>


</body>
</html>
